Bowtie Solexa data analysis help

[Ka123$]

Has anyone used Bowtie software to do the analysis?
I have solexa data that I have aligned to one of the hu chromosomes. When I try to map using bowtie-maptool it gives me an error saying :

Could not find an id to map reference name "gi|12345678|ref|NT_12346727.12|" to.

Any clues why? Is there any other way of mapping this?

[ECO]

Didn't belong where you put it, so it's here now.

[Ka123$]

thanks so much!

[Ben Langmead]

Has anyone used Bowtie software to do the analysis?
I have solexa data that I have aligned to one of the hu chromosomes. When I try to map using bowtie-maptool it gives me an error saying :

Could not find an id to map reference name "gi|12345678|ref|NT_12346727.12|" to.

Any clues why? Is there any other way of mapping this?

The program used to align reads is called 'bowtie'. 'bowtie-maptool' is for converting among Bowtie's various output formats.

A very good place to start is by looking at Bowtie's Getting Started Guide and Manual online.

Thanks,
Ben

[Ka123$]

Thanks Ben

after align do we do map on a different software?
I thought bowtie can do the mapping too.....
Have u come across a segmentation error when u run maptool?

again thanks for your input!

[simonandrews]

after align do we do map on a different software?
I thought bowtie can do the mapping too.....

I think there may be a problem with terminology here. What do you mean by mapping? Most people use mapping to describe the process of aligning a read against a reference sequence (eg an annotated genome).

In bowtie you'd use the 'bowtie' program itself to to the alignment.

[Ka123$]

File format of bowtie

Hi ,
Does anyone know what file format does the bowtie output give after aligning the solexa data to a reference.Do we need to convert this to a BED file to be able to analyse in cisGenome? or can we directly use this file in UCSC?
Thanks.

[Ka123$]

hello all

When I try coverting my bowtie to BED file using bowtie converter on http://vancouvershortr.wiki.sourcefo...t/ConvertToBed
and execute it I get a message : could not locate a bowtie index corrresponding to the name "GaP_align"
My command is:
./bowtie GaP_align . GaP_align_BED -noflag



I have my bowtie aligned reads under the GaP_align name. then why is it not able to read it from there?
Any help is appreciated.....
Thanks

[simonandrews]

When I try coverting my bowtie to BED file using bowtie converter on http://vancouvershortr.wiki.sourcefo...t/ConvertToBed
and execute it I get a message : could not locate a bowtie index corrresponding to the name "GaP_align"
My command is:
./bowtie GaP_align . GaP_align_BED -noflag

The page you linked to is for a separate application called ConvertToBed which is part of the short read analysis package. The command you included was running the actual bowtie program.

You need to install the ConvertToBed program and then run that instead.

[Ka123$]

Hi Fejes,
According to your previous blog help
"With the latest version (4.0.x), the convertToBed.jar application should be invoked as:

"java -jar /path/to/ConvertToBed.jar -input GaP_align --output /output/path/ -aligner bowtie"
"
I tried this command and it did not work. I am working on a unix server and it cannot recognise the -jar.. Also I copied the ConvertToBed into my current path and ran it nothing happend ,Error saying Main class not defined...
I am not sure If it is a java installation problem or if a main class file is not there in fp4 folder.
Also When I tried searching for the complete "http://vancouvershortr.wiki.sourcefo...t/ConvertToBed" the page does not link me to "FileConversionTools" anymore, as I could access before a couple of days...
Any suggestion will help...
Thanks in advance.

[schaffer]

Bowtie map to Ensemble gene annotations

I haven't used Bowtie, but I want to know how to convert the Bowtie mapped output to annotated Ensembl genes?
I need to be able to map to the gene and to map to 200bp upstream to the genes?
Lana

[simonandrews]

I haven't used Bowtie, but I want to know how to convert the Bowtie mapped output to annotated Ensembl genes?
I need to be able to map to the gene and to map to 200bp upstream to the genes?
Lana

You can load your data into SeqMonk, which allows you to visualise your data against an annotated genome (with the annotations all coming from Ensembl). You can also quantitate over different regions (genes, promoters etc...). It will read default bowtie output (or SAM files if you chose that option).